Contacts of the strand formed by residues 340 - 348 (chain A) in PDB entry 1CG4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A TRP* 3.6 15.8 - - - -
338A LEU* 3.4 7.1 - - - +
339A LYS* 1.3 93.3 - - + +
341A VAL* 1.3 66.2 + - - +
342A LYS* 4.7 11.2 + - - -
374A THR* 3.3 26.2 - - + +
375A MET 3.2 15.3 - - - +
376A PRO* 4.4 2.5 - - + -
377A GLY 3.4 3.4 - - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A TRP* 3.8 9.4 - - + -
335A LEU* 3.9 22.2 - - + +
338A LEU* 3.8 27.6 - - + -
340A GLU* 1.3 78.0 - - - +
342A LYS* 1.3 65.6 + - - +
374A THR* 3.5 2.7 - - - +
375A MET* 2.7 45.8 + - + +
376A PRO 4.2 8.1 - - - +
377A GLY* 4.4 7.6 - - - -
378A TRP* 4.5 6.3 - - + -
398A TYR* 3.5 35.2 - - + +
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A TRP* 3.4 66.6 - - + +
310A LEU 4.2 2.4 + - - +
340A GLU* 4.7 10.0 + - - -
341A VAL* 1.3 79.5 - - - +
343A LEU* 1.3 67.3 + - - +
372A TYR* 3.4 37.2 - - + +
373A GLU 2.8 19.1 - - - +
374A THR* 3.8 21.6 + - - -
375A MET* 4.4 1.1 - - - +
398A TYR* 4.9 2.3 + - - -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU* 3.8 15.9 - - + +
312A THR* 4.1 13.5 - - - +
342A LYS* 1.3 76.7 - - - +
344A CYS* 1.3 63.8 + - - +
345A VAL 3.1 2.3 + - - -
372A TYR* 3.5 3.3 - - - -
373A GLU* 2.9 35.5 + - + +
375A MET* 3.7 22.2 - - + -
398A TYR* 3.1 43.5 - - + +
401A ARG* 3.7 9.2 - - + -
402A ILE* 4.3 10.5 - - + -
405A LEU* 3.3 32.1 - - + -
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR* 3.3 25.1 - - + -
310A LEU 3.2 8.1 + - - -
311A ASP* 3.6 20.6 - - - +
312A THR* 2.9 27.0 + - - -
313A VAL* 3.6 3.0 + - - -
343A LEU* 1.3 70.9 - - - +
345A VAL* 1.3 56.7 + - - +
346A ALA 3.4 24.5 - - - -
347A TYR* 3.8 15.7 - - - -
370A PRO* 3.8 16.4 - - - -
371A ILE 3.7 5.4 - - - -
372A TYR* 3.7 10.2 - - + -
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A THR* 4.7 4.0 - - - -
313A VAL* 3.5 4.9 - - - -
316A ARG* 3.1 23.9 + - - +
343A LEU 3.1 10.1 + - - +
344A CYS* 1.3 71.5 - - - +
346A ALA* 1.3 61.2 + - + +
356A THR* 3.3 8.7 - - - +
371A ILE* 3.0 21.6 + - + +
372A TYR 4.2 13.2 - - - +
373A GLU* 3.6 23.6 - - + +
405A LEU* 3.5 39.6 - - + +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A VAL* 3.6 5.3 - - - +
344A CYS* 3.4 7.4 - - - -
345A VAL* 1.3 85.8 - - + +
347A TYR* 1.3 65.8 + - - +
354A GLU* 3.8 28.5 - - + +
355A VAL 3.5 11.2 - - - +
356A THR* 3.9 9.9 - - + -
371A ILE* 2.9 31.9 + - + -
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Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PRO* 3.8 19.5 - - + +
311A ASP* 2.6 32.5 + - - -
313A VAL* 3.6 26.9 - - + +
314A ALA* 3.8 2.4 - - - +
344A CYS* 3.8 9.4 - - - -
346A ALA* 1.3 81.3 - - - +
348A ARG* 1.3 61.8 + - - +
349A MET* 4.3 7.2 - - - -
354A GLU* 3.4 4.0 - - - +
355A VAL* 2.6 53.4 + - + +
357A THR 3.8 13.9 - - - -
358A THR* 3.7 13.1 - - + +
359A PRO* 3.9 13.0 - - + -
365A TRP* 3.3 33.4 - + - -
368A VAL* 4.3 12.6 - - + -
369A GLU 3.6 7.6 - - - +
371A ILE* 3.8 2.5 - - - -
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 1.3 71.5 - - - +
349A MET* 1.3 67.1 + - - +
352A GLY* 2.7 43.4 + - - -
353A ARG 3.7 1.8 - - - -
354A GLU* 3.5 38.2 + - - +
367A GLY 4.5 0.7 - - - +
368A VAL* 3.6 2.6 - - - -
369A GLU* 2.9 45.0 + - + +
371A ILE* 3.7 21.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il